Scientists sequence genome of 700,000-year-old horse

Genome analysis indicates the ancestor of all living horses, donkeys and zebras lived about four million years ago. (Photo by C. Lagattuta)

Beth Shapiro (Photo by C. Lagattuta)

An international team of scientists has sequenced the genome of an ancient horse that lived 700,000 years ago in the early Middle Pleistocene epoch. It is by far the oldest genome scientists have been able to sequence (almost ten times older than the previous record) and was obtained from DNA fragments extracted from a bone scientists recovered from permafrost in Canada's Yukon Territory.

The team's analysis of the ancient horse's genome, published June 26 in Nature, sheds light on the evolution of horses and the relationship between domestic horses and the wild Przewalski horse.

Researchers at UC Santa Cruz led by Beth Shapiro, associate professor of ecology and evolutionary biology, were involved in several aspects of the study, including the characterization of the field site where the bone was found (at Thistle Creek in the Yukon) and the sequencing, assembly, and analysis of the ancient horse's genome. Mathias Stiller, a postdoctoral researcher in Shapiro's lab, sequenced complete mitochondrial genomes (small cellular genomes separate from the nuclear chromosomes) of other ancient horses, which the researchers used to confirm the exceptionally old age of the Thistle Creek horse that is the main focus of the study.

"This is exciting in that it pushes back the time in which DNA is recoverable by nearly an order of magnitude," Shapiro said. "The bone was recovered from the oldest known permafrost, so it is a special case. Had it not been frozen for the entire duration of that 700,000 years, I doubt that any recoverable DNA would have survived. As a consequence, it's a real treasure!"

First author Ludovic Orlando of the Center for GeoGenetics at the Natural History Museum of Denmark led the project and coordinated the efforts of researchers around the world. The team was able to track major genomic changes in the evolution of the horse lineage over the past 700,000 years by comparing the genome of the Thistle Creek horse with the genomes of a 43,000-year-old Late Pleistocene horse, six present-day horses, and a donkey.

The researchers estimated how fast mutations accumulated over time in the horse lineage and calibrated a genome-wide mutation rate to use as an evolutionary "clock." This revealed that the last common ancestor of all modern horses, donkeys, and zebras lived about 4 to 4.5 million years ago, twice as long ago as previously thought. In addition, this new clock revealed multiple episodes of severe demographic fluctuation in horse history, in phase with major climatic changes such as the last glacial maximum about 20,000 years ago.

The researchers also analyzed the genome to look for evidence of interbreeding between modern domestic horses and the Przewalski horse, a wild horse of the Mongolian steppes that is physically distinctive and has an extra pair of chromosomes. The evolutionary origin of this horse, discovered by the Western world in the second half of the nineteenth century, has remained a mystery. It almost became extinct in the wild by the mid-1950s, but was saved by massive conservation efforts. James Cahill, a Ph.D. student in Shapiro's lab, assisted in an analysis indicating that pure Przewalski horse lineages, with no detectable levels of admixture with domestic breeds, are still living today. The study found that the Przewalski and domestic horse populations diverged sometime between 38,000 and 72,000 years ago.

The study also identified genomic regions in domestic horse breeds that show low levels of genetic variation compared to the Przewalski horse and could correspond to genetic variants selected early on in the domestication process.

"In order to really tease out the evolutionary changes associated with horse domestication, we need to know where the genes are in the genome and what they do, which means we need a better annotated genome of the modern horse," Shapiro said. "But using these older genomes is a great start--it can point us to regions of the genome that appear to have been evolving under selection for tens or even hundreds of thousands of years. Now we just have to figure out why."